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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbKegg_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/biodbKegg.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbKegg/DESCRIPTION’ ... OK
* this is package ‘biodbKegg’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbKegg’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
KeggEnzymeConn   9.323  0.365  11.313
KeggCompoundConn 6.118  0.676   9.769
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
    6.         └─private$searchByMass(ids = ids, fields = fields)
    7.           └─self$wsFind(query = query, option = option, retfmt = "ids.no.prefix")
    8.             └─self$getBiodb()$getRequestScheduler()$sendRequest(request)
    9.               └─cch$saveContentToFile(...)
   10.                 └─private$doSaveContentToFile(...)
   11.                   └─biodb:::saveContentsToFiles(file.paths, content)
   12.                     └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
   13.                       └─biodb `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
   14.                         └─base::cat(cnt, file = f)
   15.                           └─base::file(file, ifelse(append, "a", "w"))
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 1581 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/biodbKegg.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbKegg
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘biodbKegg’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbKegg)

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbKegg)
> Sys.setenv(TESTTHAT_REPORTER = "summary")
> test_check("biodbKegg")
trying URL 'https://www.kegg.jp/kegg/pathway/map/map00260.png'
downloaded 44 KB

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 1581 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error (???): ppm tolerance works in annotateMzValues() ──────────────────────
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
  3.   └─conn$annotateMzValues(...)
  4.     └─self$searchForEntries(fieldsFilter, max.results = max.results)
  5.       └─private$doSearchForEntries(fields = fields, max.results = max.results)
  6.         └─private$searchByMass(ids = ids, fields = fields)
  7.           └─self$wsFind(query = query, option = option, retfmt = "ids.no.prefix")
  8.             └─self$getBiodb()$getRequestScheduler()$sendRequest(request)
  9.               └─cch$saveContentToFile(...)
 10.                 └─private$doSaveContentToFile(...)
 11.                   └─biodb:::saveContentsToFiles(file.paths, content)
 12.                     └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 13.                       └─biodb `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 14.                         └─base::cat(cnt, file = f)
 15.                           └─base::file(file, ifelse(append, "a", "w"))

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 1581 ]
Error: Test failures
Execution halted